Isomerization Channels Research Articles

Investigation of the reactions of U, U+and U2+with ammonia: mechanisms and topological analysis

Reactions of uranium atom and ions (U, U+ and U2+) with NH3 have been studied in the gas phase using density functional calculations. The detailed description of reaction mechanisms and diverse topological analysis provide insights into the chemistry of uranium species. The reaction pathways leading to different products are closely examined. In the case of U and U+ reacting with NH3, the isomerization channel (the products are H2UNH and H2UNH+, respectively) and H2 elimination channel (decomposed to UNH + H2 and UNH+ + H2) were investigated. In the U2+ + NH3 reaction, UNH2+ was found to be the only product generated by the dehydrogenation of the HUNH22+ intermediate. The obtained results are compared to recent experimental studies. Bonding evolution along with the reactions was investigated using diverse topological analyses, including electron localization function, atoms in molecules, and natural bond orbital. A comparison with other results reported in the literature for similar systems, such as the reactions of uranium species with NH3, H2O and CH4, is made to underline the similarities and differences of the reaction mechanisms.

Reaction mechanism and product branching ratios of the CH + C₃H₈ reaction: a theoretical study.

The C4H9 potential energy surface accessed by the reaction of methylidyne radical, CH (X(2)Π), with propane, C3H8, including possible intermediates, transition states and dissociation products, has been studied by ab initio and density functional calculations at the CCSD(T)/CBS//B3LYP/6-311G(d,p) level of theory. The computed relative energies and molecular parameters were utilized to calculate collision-energy-dependent unimolecular rate constants at the zero-pressure limit for isomerization and dissociation channels of the C4H9 adducts formed in the entrance reaction channels. The rate constants were used to evaluate the product branching ratios in the CH + C3H8 reaction under single-collision conditions. The results show that the reaction can produce mostly ethene (C2H4) + ethyl radical (C2H5) and propene (C3H6) + methyl radical (CH3), and up to 14% of various butene isomers (C4H8) + H. The product branching ratios are sensitive to the initial reaction adduct (a butyl radical, C4H9) formed in the entrance channels via barrierless insertion of the CH radical into the terminal and middle C-H bonds of propane or, possibly, into the single C-C bonds. A more definite answer on relative contributions of various available CH insertion channels can be obtained through ab initio quasiclassical trajectory calculations, which are proposed for the future. The results allowed us to conclude that the CH + C3H8 reaction does not result in major amounts in the direct growth of the carbon-skeleton to four-carbon C4H8 products via the CH-for-H exchange because C-C bond cleavages in C4H9 radicals are generally more preferable than C-H bond cleavages.

Gas‐phase water activation by Th atom: Reaction mechanisms and topological analysis

Density functional theory calculations were performed to investigate the gas‐phase reaction of Th atom with water. Three reaction pathways were identified, which leads to the formation of ThOH + H, ThO + H2, and H2ThO. The latter two are generated via the intermediate HThOH, and the H2ThO specie is generated from the isomerization of the HThOH intermediate. A thorough description of the reaction mechanism taking into account different possible spin states together with analysis of the electronic factors offer insights into the reactivity of the actinides atom. The obtained results are compared with the available experimental data. The three reaction pathways were found to be exothermic, in which the isomerization channel was observed with best thermochemical conditions around 123.9 kcal/mol. The nature of the chemical bonding evolution along the reaction pathways was studied using topological analysis including electron localization function, atoms‐in‐molecules, and natural bond orbital. © 2014 Wiley Periodicals, Inc.

Synthetic Control of Retinal Photochemistry and Photophysics in Solution

Understanding how molecular structure and environment control energy flow in molecules is a requirement for the efficient design of tailor-made photochemistry. Here, we investigate the tunability of the photochemical and photophysical properties of the retinal-protonated Schiff base chromophore in solution. Replacing the n-butylamine Schiff base normally chosen to mimic the saturated linkage found in nature by aromatic amines results in the reproduction of the opsin shift and complete suppression of all isomerization channels. Modification of retinal by directed addition or removal of backbone substituents tunes the overall photoisomerization yield from 0 to 0.55 and the excited state lifetime from 0.4 to 7 ps and activates previously inaccessible reaction channels to form 7-cis and 13-cis products. We observed a clear correlation between the presence of polarizable backbone substituents and photochemical reactivity. Structural changes that increase reaction speed were found to decrease quantum yields, and vice versa, so that excited state lifetime and efficiency are inversely correlated in contrast to the trends observed when comparing retinal photochemistry in protein and solution environments. Our results suggest a simple model where backbone modifications and Schiff base substituents control barrier heights on the excited-state potential energy surface and therefore determine speed, product distribution, and overall yield of the photochemical process.

Ozone and organic nitrates over the eastern United States: Sensitivity to isoprene chemistry

AbstractWe implement a new isoprene oxidation mechanism in a global 3‐D chemical transport model (GEOS‐Chem). Model results are evaluated with observations for ozone, isoprene oxidation products, and related species from the International Consortium for Atmospheric Research on Transport and Transformation aircraft campaign over the eastern United States in summer 2004. The model achieves an unbiased simulation of ozone in the boundary layer and the free troposphere, reflecting canceling effects from recent model updates for isoprene chemistry, bromine chemistry, and HO2 loss to aerosols. Simulation of the ozone‐CO correlation is improved relative to previous versions of the model, and this is attributed to a lower and reversible yield of isoprene nitrates, increasing the ozone production efficiency per unit of nitrogen oxides (NOx ≡ NO + NO2). The model successfully reproduces the observed concentrations of organic nitrates (∑ANs) and their correlations with HCHO and ozone. ∑ANs in the model is principally composed of secondary isoprene nitrates, including a major contribution from nighttime isoprene oxidation. The correlations of ∑ANs with HCHO and ozone then provide sensitive tests of isoprene chemistry and argue in particular against a fast isomerization channel for isoprene peroxy radicals. ∑ANs can provide an important reservoir for exporting NOx from the U.S. boundary layer. We find that the dependence of surface ozone on isoprene emission is positive throughout the U.S., even if NOx emissions are reduced by a factor of 4. Previous models showed negative dependences that we attribute to erroneous titration of OH by isoprene.

Ab initio studies of isomerization and dissociation reactions of methyl peroxynitrate

Using the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p) method, we calculated the detailed potential energy surfaces (PESs) for the unimolecular isomerization and decomposition of methyl peroxynitrate (CH3O2NO2). The results show that there are the two most stable isomers, IS1a and IS1b, which are a pair of mirror image isomers. From IS1a and IS1b, different isomerization and unimolecular decomposition reaction channels have been studied and discussed. Among them, the predominant thermal decomposition pathways are those leading to CH3O2 + NO2 and cis-CH3ONO + O2. The former is the lowest-energy path through the direct O–N bond rupture in IS1a or IS1b. The PES along the O–N bond in IS1a has been scanned, where the energy of IS1a reaches maximum value of 23.5 kcal/mol when the O–N bond is stretched to about 2.8 A. This energy is 2.7 kcal/mol larger than the O–N bond dissociation energy (BDE) and 2.8 kcal/mol larger than the experimental active energy. In addition, because the energy barriers of IS1a isomerization to IS2a are 23.8 kcal/mol, close to the 20.8 kcal/mol O–N BDE in IS1a or IS1b, the isomerization reaction may compete with the direct bond rupture dissociation reaction.

Signatures of Isomerization in Photodissociation of trans- Crotonaldehyde Probed by Multiphoton Ionization Mass Spectrometry

We report the observation of new isomerization effects in the UV-photodissociation of trans-crotonaldehyde upon multiphoton excitation by the third harmonic (355 nm) pulses of a Nd:YAG laser. A time-of-flight mass spectrometric analysis reveals formation of acetaldehyde, acetyl, and methoxy radical cations as signatures of isomerization processes. A small segment of the multiphoton ionization spectrum of jet-cooled crotonaldehyde is recorded by tuning the laser frequency around 355 nm. An oxetene type transient intermediate in the ground state has been considered for acetaldehyde formation following a photochemical model suggested earlier (Reguero ; et al. J. Am. Chem. Soc. 1994, 116, 2101-2114) for such compounds. Likewise, for methoxy radical formation, a trans-cis isomerization about the C═C double bond has been considered in a triplet surface. Electron ionization mass spectra of the compound are also recorded by varying the electron kinetic energy in the range 11-70 eV. Ionic fragments in the mass spectra of the two ionization processes are dramatically different. Our suggested mechanisms for isomerization and fragmentation channels are substantiated by density functional theory calculations. Combined experimental and calculated data lead us conclude that isomerization occurs in neutral potential energy surfaces prior to dissociation and photoionization.

Kinetics of Decomposition and Isomerization of Methylcyclohexane: Starting Point for Studying Monoalkylated Cyclohexanes Combustion

Monoalkylated cyclohexanes are one of the typical constituents existing in practical fuels, especially in jet fuel. As the first step to study the combustion chemistry of monoalkylated cyclohexanes, the unimolecular reactions of methylcyclohexane (MCH) were investigated by combined theoretical calculations and experimental measurements for MCH pyrolysis and flames in the present work. The temperature- and pressure-dependent kinetics of unimolecular reactions of MCH including its dissociation and isomerization channels were computed by high-level quantum chemical calculations and Rice–Ramsperger–Kassel–Marcus/master equation simulations, which also reveal the competition relationship between the two channels. The theoretical predictions were examined by the experimental observations including species identification measured by photoionization efficiency spectra. The presented unimolecular reaction mechanism and corresponding temperature- and pressure-dependent rate constants provide a useful reference for further exploring combustion chemistry of cyclohexanes by kinetic modeling.

Excited state dynamics of Photoactive Yellow Protein chromophores elucidated by high-resolution spectroscopy and ab initio calculations

We report on experimental high-resolution spectroscopic studies in combination with advanced theoretical calculations that focus on the excited-state dynamics of various forms of the chromophore of the Photoactive Yellow Protein (PYP), and the dependence of these dynamics on conformational and isosteric structure, as well as the biological environment. Three-colour nanosecond multiphoton ionization pump-probe studies confirm and extend previous conclusions that the dominant decay channel of the lowest excited pipi* state (the so-called V' state) of methyl-4-hydroxycinnamate is picosecond internal conversion to the adiabatically lower nPi* state, and enable us to resolve apparent contradictions with picosecond pump-probe studies. Comparison of multiphoton ionization and laser induced fluorescence excitation spectra leads to the assignment of the hitherto elusive excitation spectrum of the V(pipi*) state. Complexation of methyl-4-hydroxycinnamate with water radically changes the excited-state dynamics; internal conversion to the npi* state is absent, and bond isomerization channels instead play a prominent role. Excited states of the thio-ester compound, the form in which the chromophore is present in PYP, have till the present study remained out of reach of gas-phase studies. The excitation spectra obtained here show a broad, almost structureless band system, giving evidence for enhanced nonradiative decay channels. The gas-phase results will be discussed in the context of results from ultrafast studies on these two chromophores in solution.

SEARCHING FOR INTERSTELLAR MOLECULE BUTATRIENYLIDENE IN REACTION C2+ C2H4

We investigated the reaction C2(X1Σ+g/a3Πu) + C2H4 at collision energy 5.0 kcal mol−1 in a crossed molecular-beam apparatus using selective photoionization. Time-of-flight and photoionization spectra of products C4H3 and C4H2 were measured. From the best simulation of product time-of-flight spectra, a low-energy-biased translational-energy distribution and an isotropic angular distribution are derived for product channels C4H3 + H and C4H2 + H2 that have average translational-energy releases of 11 and 20 kcal mol−1, respectively. Product C4H3 is identified as H2CCCCH because its ionization threshold 8.0 ± 0.2 eV and maximal translational-energy release 42 kcal mol−1 coincide with that of product channel H2CCCCH + H. H2CCCC (butatrienylidene) and HCCCCH (diacetylene) might have contributions to product C4H2; both isomers have ionization energies near the measured ionization threshold 10.0 ± 0.2 eV and the maximal translational-energy release 62 kcal mol−1 is within the energetic limits of both isomeric product channels. Nonetheless, channel H2CCCC + H2 is suggested to be more dominant than channel HCCCCH + H2 because the maximal translational-energy release is in good agreement with the available energy of the former channel and the former channel is 3.8 times the branching ratio of the later channel predicted by Rice–Ramsperger–Kassel–Marcus calculations. C4H2 is identified for the first time in the barrierless reaction C2 + C2H4 which has never been considered in any astronomical chemical networks. This work sheds new light on the formation of butatrienylidene/diacetylene in cold interstellar media where C2 and C2H4 are abundant.

On the structures, stabilities, and potential energy surfaces of planar BnN (n = 1–6) clusters

The structures, stabilities, and potential energy surfaces (PESs) of the low-lying isomers of planar BnN (n=1–6) clusters are searched at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. The lowest-energy structures (1a–6a) of planar BnN (n=1–6) are located. It is worthy to note a structural transition occurring in the series of BnN (n=1–6) clusters upon increase of the boron content from n=3 to n=4. The evolution of the binding energy per atom, incremental binding energy, and second order difference of total energy with the size of BnN reveals that the lowest-energy isomers 2a (B2N) and 5a (B5N) are highly stable. Results demonstrate that the stability of lowest-energy isomers of BnN (n=1–6) is attributed to the delocalized π, σ-radial, and σ-tangential molecular orbitals (MOs) interactions. The isomers of BnN (n=4–6) with planar multicoordinate boron or nitrogen are unfavorable in energy. The double aromaticity of isomer 3d of B3N is discussed in terms of valence molecular orbital, electron localization function (ELF) and adaptive natural density partitioning (AdNDP), and NICS analyses. Interestingly, some isomer pairs can be transferred directly to each other by two or three isomerization channels. Some isomers of BnN with large thermodynamic and kinetic stability are predicted in terms of their total energies and potential energy surfaces, which is important for future experimental studies.

Relaxation Dynamics and Structural Characterization of Organic Nanobelts with Aggregation-Induced Emission

We prepared the fluorescent nanobelts of cyano-substituted 1,4-distyrylbenzene derivative (CNDSB) with the reprecipitation method. CNDSB is nonemissive in solution but with strong aggregation-induced emission (AIE) in belt-like structure. The molecular structure predicted by quantum chemical calculations indicates a twisted conformation of CNDSB monomer, while the solid-state X-ray structure of the CNDSB crystal features herringbone-type arrangement and three benzene rings arrange in nearly planar conformation. Femto- and picosecond time-resolved fluorescence spectroscopy are implemented to study the photophysics and the origin of the AIE effect in CNDSB nanobelts. The fluorescence quenching of CNDSB in THF solution arises from the efficient nonradiative isomerization channel. In this study, the fluorescence decay of CNDSB embedded in poly(methyl methacrylate) matrix is slowed down due to the restriction of intramolecular motions in the solid matrix. In nanobelt structure, the fluorescence lifetime further increases due to the intermolecular interaction between H-type aggregates. Both the steady-state and time-resolved studies suggests that there are at least two different packing structures might exist in nanobelts, and the relative composition of these two different structures gradually changes in different sizes of nanobelts.

Chemical Structures of Low-Pressure Premixed Methylcyclohexane Flames as Benchmarks for the Development of a Predictive Combustion Chemistry Model

The chemical compositions of three low-pressure premixed flames of methylcyclohexane (MCH) are investigated with the emphasis on the chemistry of MCH decomposition and the formation of aromatic species, including benzene and toluene. The flames are stabilized on a flat-flame (McKenna type) burner at equivalence ratios of φ = 1.0, 1.75, and 1.9 and at low pressures between 15 Torr (= 20 mbar) and 30 Torr (= 40 mbar). The complex chemistry of MCH consumption is illustrated in the experimental identification of several C7H12, C7H10, C6H12, and C6H10 isomers sampled from the flames as a function of distance from the burner. Three initiation steps for MCH consumption are discussed: ring-opening to heptenes and methyl-hexenes (isomerization), methyl radical loss yielding the cyclohexyl radical (dissociation), and H abstraction from MCH. Mole fraction profiles as a function of distance from the burner for the C7 species supplemented by theoretical calculations are presented, indicating that flame structures resulting in steeper temperature gradients and/or greater peak temperatures can lead to a relative increase in MCH consumption through the dissociation and isomerization channels. Trends observed among the stable C6 species as well as 1,3-pentadiene and isoprene also support this conclusion. Relatively large amounts of toluene and benzene are observed in the experiments, illustrating the importance of sequential H-abstraction steps from MCH to toluene and from cyclohexyl to benzene. Modeled results using the detailed chemical model of Pitz et al. (Proc. Combust. Inst.2007, 31, 267–275) are also provided to illustrate the use of these data as a benchmark for the improvement or future development of a MCH mechanism.

High-Pressure Rate Rules for Alkyl + O2 Reactions. 1. The Dissociation, Concerted Elimination, and Isomerization Channels of the Alkyl Peroxy Radical

The reactions of alkyl peroxy radicals (RO(2)) play a central role in the low-temperature oxidation of hydrocarbons. In this work, we present high-pressure rate estimation rules for the dissociation, concerted elimination, and isomerization reactions of RO(2). These rate rules are derived from a systematic investigation of sets of reactions within a given reaction class using electronic structure calculations performed at the CBS-QB3 level of theory. The rate constants for the dissociation reactions are obtained from calculated equilibrium constants and a literature review of experimental rate constants for the reverse association reactions. For the concerted elimination and isomerization channels, rate constants are calculated using canonical transition state theory. To determine if the high-pressure rate expressions from this work can directly be used in ignition models, we use the QRRK/MSC method to calculate apparent pressure and temperature dependent rate constants for representative reactions of small, medium, and large alkyl radicals with O(2). A comparison of concentration versus time profiles obtained using either the pressure dependent rate constants or the corresponding high-pressure values reveals that under most conditions relevant to combustion/ignition problems, the high-pressure rate rules can be used directly to describe the reactions of RO(2).

Medium Effects on the Direct Cis−Trans Photoisomerization of 1,4-Diphenyl-1,3-butadiene in Solution

Quantum yields for the photoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB), determined in benzene, cyclohexane, methylcyclohexane, hexane, and perfluorohexane, confirm the low values reported earlier for benzene and cyclohexane and reveal even lower values in the last two solvents. In contrast to trans-stilbene (t-St), fluorescence and torsional relaxation leading to photoisomerization do not account exclusively for S(1)tt-DPB decay. Competing radiationless singlet excited-state decay pathways exist in tt-DPB, which do not lead to photoisomerization and may not involve large-amplitude torsional motions. Our results invalidate analyses of tt-DPB fluorescence quantum yields and lifetimes that assign all radiationless decay to the isomerization channel. Gas-phase chromatography analysis of tt-DPB photoisomerization in hexane shows the reaction to be concentration-independent and reveals, for the first time, a significant, two-bond photoisomerization pathway, φ(tt→tc) = 0.092 and φ(tt→cc) = 0.020. The dominant one-bond-twist (OBT) process is accompanied by a bicycle pedal (BP) process that accounts for almost 20% of tt-DPB photoisomerization. The OBT tt-DPB photoisomerization quantum yield is largest in benzene (Bz) and smallest in perfluorohexane (PFH). Contrary to expectations, reduction in medium friction in PFH is accompanied by a decrease in φ(tt→tc). The 1(1)B(u)/2(1)A(g) order and energy gap appear to control the contribution of torsional relaxation to radiationless decay. Lowering the 1(1)B(u) energy as in Bz favors photoisomerization. Reversal of the 1(1)B(u)/2(1)A(g) order in PFH is accompanied by short τ(f) and small φ(f) and φ(tt→tc) values that suggest the presence of competing 2(1)A(g) → 1(1)Ag relaxation paths that are unproductive with respect to photoisomerization. We conclude that the Birks extension to diphenylpolyenes of the Orlandi-Siebrand cis-trans photoisomerization mechanism is not valid. Photoisomerization appears to occur in the 1(I)B(u) state, and we argue that this applies to t-St as well.

Theoretical mechanistic study on the reaction of CN radical with HNCN

The mechanism for the reaction of the cyanogen radical (CN) with the cyanomidyl radical (HNCN) has been investigated theoretically. The electronic structure information of the singlet and triplet potential energy surfaces (PESs) is obtained at the B3LYP/6-311+G(3df,2p) level, and the single-point energies are refined at the CCSD(T)/6-311+G(3df,2p) level as well as by multilevel MCG3-MPWB method. The calculations show that the C atom of CN additions to middle- and end-N atoms of HNCN are two barrierless association processes leading to the energy-rich intermediates IM1 HN(CN)CN and IM2 HNCNCN, respectively, on the singlet PES. The higher barriers of the subsequent isomerization and dissociation channels from IM1 and IM2 indicate that these two intermediates, which have considerably thermodynamic and kinetic stability, are the dominant product at high pressure. While at low pressure, the most favorable product is P(2) H + NCNCN, which will be formed from both IM1 and IM2 via direct dissociation processes by the H-N bond rupture, and the secondary feasible product is P(4) HCN + (1) NCN, while P(5) HCCN + N(2) and P(6) HCNC + N(2) are the least competitive products. On the triplet PES, P(14) NCNC + HN may be a comparable competitive product at high temperature. In addition, the comparison between the mechanisms of the CN + HNCN and OH + HNCN reactions is made. The present results will enrich our understanding of the chemistry of the HNCN radical in combustion processes and interstellar space.

Effect of the N-terminal basic residue on facile Cα–C bond cleavages of aromatic-containing peptide radical cations

Fragmentation of radical cationic peptides [R(G)(n-2)X(G)(7-n)]˙(+) and [R(G)(m-2)XG]˙(+) (X = Phe or Tyr; m = 2-5; n = 2-7) leads selectively to a(n)(+) product ions through in situ C(α)-C peptide backbone cleavage at the aromatic amino acid residues. In contrast, substituting the arginine residue with a less-basic lysine residue, forming [K(G)(n-2)X(G)(7-n)]˙(+) (X = Phe or Tyr; n = 2-7) analogs, generates abundant b-y product ions; no site-selective C(α)-C peptide bond cleavage was observed. Studying the prototypical radical cationic tripeptides [RFG]˙(+) and [KFG]˙(+) using low-energy collision-induced dissociation and density functional theory, we have examined the influence of the basicity of the N-terminal amino acid residue on the competition between the isomerization and dissociation channels, particularly the selective C(α)-C bond cleavage viaβ-hydrogen atom migration. The dissociation barriers for the formation of a(2)(+) ions from [RFG]˙(+) and [KFG]˙(+)via their β-radical isomers are comparable (33.1 and 35.0 kcal mol(-1), respectively); the dissociation barrier for the charge-induced formation of the [b(2)- H]˙(+) radical cation from [RFG]˙(+)via its α-radical isomer (39.8 kcal mol(-1)) was considerably higher than that from [KFG]˙(+) (27.2 kcal mol(-1)). Thus, the basic arginine residue sequesters the mobile proton to promote the charge-remote selective C(α)-C bond cleavage by energetically hindering the competing charge-induced pathways.

DFT and ab initio theoretical study for the CF 3S + CO reaction

The potential energy surface for the reaction of CF 3S with CO is calculated at the G4//B3LYP/6–311++G(d,p) level of theory. The results show that F-abstraction and addition–elimination mechanisms are involved, and the latter one is dominant thermodynamically and kinetically. The dominant channel is the reactant addition to form CF 3SCO, and then decomposes to CF 3 + OCS. While the direct F-abstraction channel and CF 3SCO isomerization channel are not significant for the title reaction due to higher barriers involved. The comparisons among four reactions of C X 3 Y + CO ( X = H, F; and Y = O, S) are made to imply the similar and different properties and reactivities of the same family elements and the F- and S-substituted derivatives.

ChemInform Abstract: Is the Nonradiative Decay of S1 cis-Stilbene Due to the Dihydrophenanthrene Isomerization Channel? Suggestive Evidence from Photophysical Measurements on 1,2-Diphenylcycloalkenes.

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Theoretical Study of Initial Adsorptions and Subsequent Surface Rearrangements of H−C≡C−OH on Si(100)-2 × 1 Surface

The surface adsorption reactions of hydroxyl acetylene (H−C≡C−OH) on Si(100)-2 × 1 surface were theoretically investigated with the help of CASSCF and MRMP2 theories. In addition to the well-established [2 + 2] cycloaddition of acetylene, O−H, C−O, and C−H bond cleavage reactions were found, demonstrating that acid−base type reactions of acetylene are important. The OH substitution opens two subsequent surface isomerization channels from the [2 + 2] cycloaddition product, which yield both kinetically as well as thermodynamically the most favorable surface ketene product. Consequently, the major surface product of hydroxyl acetylene is predicted to be the surface ketene rather than the expected [2 + 2] product.